Hej,
I have an RNAseq dataset (single end) from a mouse model heterozygous for a trapped-gene. The construct is located between exon 1 and 2 of our target gene and any transcripts derived from this allele should be spliced from exon 1 to the construct, which contains a polyA signal to terminate transcription.
When comparing the expression levels to wildtypes, no overal difference in expression of the target gene is found. We believe it might be due to exon 1 being present in both wildtype allele and knockout allele.

We wish to count exon reads (for exon 2-12) for our gene of interest, and compare the expression levels of between genotypes. Anyone can help me? What tool to use, which settings?